1dgs

About this Structure
1DGS is a 2 chains structure with sequences from Thermus filiformis. The July 2004 RCSB PDB Molecule of the Month feature on DNA Ligase by David S. Goodsell is 10.2210/rcsb_pdb/mom_2004_7. Full crystallographic information is available from OCA.

This protein contains 4 distinct domains. Subdomain 1a consists mostly of alpha helices. Subdomain 1b contains antiparallel beta sheets surrounded by more alpha helices. Domain 2 is an OB type structural fold. Subdomain 3a is mostly a zinc finger region with a beta hairpin. Subdomain 3b consists of four helix-hairpin-helix structural motifs. Domain 4 is part of the BRCT superfamily. The 4 domains combine to form a ring with a center about as large as DNA, which is logical given this protein's importance in DNA replication.

The OB structural fold in domain 2 is typical of proteins which interact with DNA. The presence of a zinc finger in domain 3a is often indicative of a receptor protein, so it is possible that the zinc finger is used to recognize breaks in the DNA strand. Domain 3b is likely representative of a binding site for DNA. Domain 4 shows some looseness in structure without being totally disordered. This suggests that it may be the opening that allows the protein to get around the DNA in the first place before domain 4 clamps down and surrounds the DNA strand.

Possible Method of Action
All of this paints a picture for how the protein acts on DNA. The protein opens domain 4, slips itself around the DNA strand, and moves down the strand until it finds a damaged portion. It then rearranges itself to put the damaged region in the active sites where it then repairs the DNA strand.

Reference
Page seeded by OCA on Thu Jan 21 09:29:13 2010